Are adenine strands helical H-aggregates?

On the basis of our quantum mechanical calculation, we propose that homogeneous single-stranded adenine bases (Ade-DNA) form helical H aggregates, and the photoexcited states can be described as Frenkel excitons. The calculated excitonic coupling between adjacent transition dipoles is in good agreement with the measured absorption spectrum of 20-base homogeneous adenine stacks that exhibits a blue shift of 2.6 nm relative to that of the monomeric species.

Time-dependent density-functional theory/localized density matrix method for dynamic hyperpolarizability

Time-dependent density-functional theory/localized density matrix method (TDDFT/LDM) was developed to calculate the excited state energy, absorption spectrum and dynamic polarizability. In the present work we generalize it to calculate the dynamic hyperpolarizabilities in both time and frequency domains. We show that in the frequency domain the 2n+1 rule can be derived readily and the dynamic hyperpolarizabilities are thus calculated efficiently. Although the time-domain TDDFT/LDM is time consuming, its implementation is straightforward because the evaluation of the derivatives of exchange-correlation potential with respect to electron density is avoided. Moreover, the time-domain method can be used to simulate higher order response which is very difficult to be calculated with the frequency-domain method.

Improving the accuracy of density-functional theory calculation: the genetic algorithm and neural network approach

The combination of genetic algorithm and neural network approach (GANN) has been developed to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation and GANN correction approach has been applied to evaluate the optical absorption energies of 150 organic molecules. The neural network approach reduces the root-mean-square (rms) deviation of the calculated absorption energies of 150 organic molecules from 0.47 to 0.22 eV for the TDDFTB3LYP6-31G(d) calculation, and the newly developed GANN correction approach reduces the rms deviation to 0.16 eV.

[Identification of sulphur residue in chrysanthemum by Fourier transform infrared spectroscopy]

Qi and Huai chrysanthemum samples processed in different ways were discriminated by means of Fourier transform infrared (FTIR) spectroscopy. It was shown that different processing methods may result in the variation of relative content of effective components in chrysanthemum. The variation of chemical structure may also occur. And the variations can be reflected differently on the transform infrared spectra. The dry chrysanthemum smoked with sulphur had different characters in the vibration frequency and shape of IR from other samples at 1 600 and 1 060 cm(-1), and showed static characteristic absorptions at 922, 818 and 777 cm(-1), which were stronger than others. The chrysanthemum processed in different ways showed differences in the Fourier transform infrared spectra. The sulphur residue in chrysanthemum can be identified by FTIR without separation and abstraction. This method is not only quick and precise but also convenient and direct. Different sorts of chrysanthemum can be identified in this way.

Density matrix based time-dependent density functional theory and the solution of its linear response in real time domain

A density matrix based time-dependent density functional theory is extended in the present work. Chebyshev expansion is introduced to propagate the linear response of the reduced single-electron density matrix upon the application of a time-domain delta-type external potential. The Chebyshev expansion method is more efficient and accurate than the previous fourth-order Runge-Kutta method and removes a numerical divergence problem. The discrete Fourier transformation and filter diagonalization of the first-order dipole moment are implemented to determine the excited state energies. It is found that the filter diagonalization leads to highly accurate values for the excited state energies. Finally, the density matrix based time-dependent density functional is generalized to calculate the energies of singlet-triplet excitations.

Structure-activity relationships of flavonoids for vascular relaxation in porcine coronary artery

Flavonoids are polyphenolic compounds that are widespread in the plant kingdom, and structure-activity relationships (SAR) for vascular relaxation effects were examined for 17 of them using porcine coronary arteries. Density functional theory was employed to calculate the chemical parameters of these compounds. The order of potency for vascular relaxation was as follows: flavones (apigenin and luteolin) >or= flavonols (kaempferol and quercetin)>isoflavones (genistein and daidzein)>flavanon(ol)es (naringenin)>chalcones (phloretin)>anthocyanidins (pelargonidin)>flavan(ol)es ((+)-catechin and (-)-epicatechin). SAR analysis revealed that for good relaxation activity, the 5-OH, 7-OH, 4'-OH, C2=C3 and C4=O functionalities were essential. Comparison of rutin with quercetin, genistin with genistein, and puerarin with daidzein demonstrated that the presence of a glycosylation group greatly reduced relaxation effect. Total energy and molecular volume were also predictive of their relaxation activities. Our findings indicated that the most effective relaxing agents are apigenin, luteolin, kaempferol and genistein. These flavonoids possess the key chemical structures demonstrated in our SAR analysis.

Maxwell's demon and Smoluchowski's trap door

A simulation has been performed to reveal the detailed dynamics and statistical behavior of a Maxwell demon of the simplest kind, a trap door held over by a spring inside a box filled with gas molecules. The role of such a demon can be controlled by tuning Smoluchowski's fluctuations. When the demon is in thermal equilibrium with the rest of the system, it fails to function as designed, and when it is separately subjected to a thermal bath with a different temperature, it creates a temperature or density gradient between the two chambers of the box it divides. As a Maxwell demon, the trap-door device creates more readily a density gradient than that of temperature.

The oscillatory characteristics of a 2C60/CNT oscillator system

The authors have studied, using molecular dynamic (MD) simulations, the oscillatory characteristics of a 2C60/CNT oscillator system, in which two C60 fullerenes oscillate inside a single walled carbon nanotube (CNT) in two basic modes, i.e., the symmetric and non-symmetric motions. In the symmetric mode, with each oscillation the two fullerenes move symmetrically from the CNT ends towards the CNT center where they bounce off each other and head back towards the ends. In the non-symmetric mode, the two fullerenes move back and forth inside the CNT crossing the center point of the CNT together with each oscillation. The simulations show that the non-symmetric oscillation mode is stable for the prescribed initial (maximum) velocities up to 300 m/s, while the symmetric oscillation mode however, experiences dynamic instabilities for a prescribed initial (maximum) velocity larger than 250 m/s. The instability takes place as a result of the transfer of energy from the translational to the rotational motion of the fullerenes. This characteristic differentiates 2C60/CNT oscillators from double-walled CNT oscillators. The rotation is primarily caused by the inter-colliding of the two fullerenes, which subjects the fullerenes to large van der Waals repelling forces. These repelling forces are not necessarily aligned perfectly along the CNT axis nor precisely pointing towards the mass centers of the fullerenes. These misalignments cause the fullerenes to rock around the CNT's axis, while their offsets from the mass centers cause the fullerenes to rotate. The rocking motion, being severely confined by the CNT, does not gain much energy itself, but instead, channels energy from translational to rotational motion. The energy channeling is found to be reversed in some very short time intervals, but the rotational motion always gains energies from the translational motion over a time interval that is long enough at the MD time scale. This feature, contrary to our experiences in the macroscopic world, appears to be unique for such nanoscopic mechanical systems.

Alleviation of ischemia-reperfusion injury in rat liver transplantation by induction of small interference RNA targeting Fas

BACKGROUND

Cellular apoptosis plays an important role in ischemia-reperfusion (I/R) injury during organ transplantation. Synthetic small interference RNA (siRNA) targeting apoptotic receptor Fas has proven effective to protect mice against hepatitis and renal I/R injury. The objective of this study is to investigate the silencing impact of Fas siRNA to alleviate I/R injury in rat liver transplantation.

MATERIALS AND METHODS

Rat hepatocytes (BRL cells) were transfected with three pairs of synthesized Fas siRNA; cells untreated and treated with GFP siRNA were taken as blank and siRNA control. The most effective Fas siRNA was chosen for in vivo experiments. Syngeneic orthotopic liver transplantation was performed in Fas siRNA group, siRNA control group, and blank control group of Sprague-Dawley rats. There were 25 pairs of rats in each group. siRNA transfection of donor rats was done with hydrodynamic injection method 48 h before liver procurement. Blood and liver samples were collected for evaluation of serum ALT levels, Fas protein and mRNA expression, and apoptosis by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining, 1, 3, 6, 12, and 24 h after liver transplantation.

RESULTS

Fas siRNA2, which inhibited Fas gene expression much more than other siRNAs, was chosen for in vivo experiment. The serum ALT levels of Fas siRNA group were much less than those of blank and siRNA control groups 1, 3, 6, 12, and 24 h after blood reperfusion, indicating diminishing ischemia-reperfusion injury. Donor livers in Fas siRNA group had substantially less cell apoptosis. The expression of Fas mRNA and protein was reduced dramatically in the Fas siRNA group compared with the other two groups.

CONCLUSION

Fas-mediated apoptosis play an important role in I/R injury of rat liver transplantation. Silencing Fas by hydrodynamic injection of siRNA holds therapeutic promise to limit I/R injury.

Mutations in BMPR-IB and BMP-15 genes are associated with litter size in Small Tailed Han sheep (Ovis aries)

The Small Tailed Han is a prolific local sheep breed in China. The bone morphogenetic protein receptor IB (BMPR-IB) gene, which affects the fecundity of Booroola Merino sheep, and the bone morphogenetic protein 15 (BMP-15) gene, which affects the fecundity of Inverdale, Hanna, Belclare, Cambridge, and Lacaune sheep, were studied as candidate genes associated with the prolificacy of Small Tailed Han sheep. Single nucleotide polymorphisms of BMPR-IB and BMP-15 genes were detected in Small Tailed Han ewes (n = 188) by PCR-RFLP. The combined effect of the 2 genes on the prolificacy of Small Tailed Han sheep was studied. The results indicated that the same FecB mutation (Q249R) occurred in the BMPR-IB gene in Small Tailed Han ewes as found in Booroola Merino ewes. The Small Tailed Han ewes with genotypes FecB(B)/FecB(B) and FecB(B)/FecB(+) had 1.40 (P < 0.01) and 1.11 (P < 0.01) more lambs, respectively, than those with genotype FecB(+)/FecB(+). The same FecX(G) mutation (Q239Ter) of the BMP-15 gene was found in Small Tailed Han ewes as in Belclare and Cambridge ewes. The Small Tailed Han ewes with the heterozygous mutant FecX(G)/FecX(+) had 0.55 (P < 0.01) more lambs than those with the wild-type FecX(+)/FecX(+). The Small Tailed Han ewes carrying mutations in both BMPR-IB and BMP-15 genes had greater litter size than those with either mutation alone. In view of our results, marker-assisted selection using both BMPR-IB and BMP-15 genes is warranted to increase litter size in sheep and will be of considerable economic value to sheep producers.

Green Luminescence Band in ZnO: Fine Structures, Electron−Phonon Coupling, and Temperature Effect

The green emission band of ZnO has been investigated by both experimental and theoretical means. Two sets of equally separated fine structures with the same periodicity (close to the longitudinal optical (LO) phonon energy of ZnO) are well resolved in the low-temperature broad green emission spectra. As the temperature increases, the fine structures gradually fade out and the whole green emission band becomes smooth at room temperature. An attempt to quantitatively reproduce the variable-temperature green emission spectra using the underdamped multimode Brownian oscillator model taking into account the quantum dissipation effect of the phonon bath is done. Results show that the two electronic transitions strongly coupled to lattice vibrations of ZnO lead to the observed broad emission band with fine structures. Excellent agreement between theory and experiment for the entire temperature range enables us to determine the dimensionless Huang-Rhys factor characterizing the strength of electron-LO phonon coupling and the coupling coefficient of the LO and bath modes.

Integration of sulphate reduction, autotrophic denitrification and nitrification to achieve low-cost excess sludge minimisation for Hong Kong sewage

An integrated anaerobic-aerobic treatment system of sulphate-laden wastewater was proposed here to achieve low sludge production, low energy consumption and effective sulphide control. Before integrating the whole system, the feasibility of autotrophic denitrification utilising dissolved sulphide produced during anaerobic treatment of sulphate rich wastewater was studied here. An upflow anaerobic sludge blanket reactor was operated to treat sulphate-rich synthetic wastewater (TOC=100 mg/L and sulphate=500 mg/L) and its effluent with dissolved sulphide and external nitrate solution were fed into an anoxic biofilter. The anaerobic reactor was able to remove 77-85% of TOC at HRT of 3 h and produce 70-90 mg S/L sulphide in dissolved form for the subsequent denitrification. The performance of anoxic reactor was stable, and the anoxic reactor could remove 30 mg N/L nitrate at HRT of 2 h through autotrophic denitrification. Furthermore, sulphur balance for the anoxic filter showed that more than 90% of the removed sulphide was actually oxidised into sulphate, thereby there was no accumulation of sulphur particles in the filter bed. The net sludge productions were approximately 0.15 to 0.18 g VSS/g COD in the anaerobic reactor and 0.22 to 0.31 g VSS/g NO3- -N in the anoxic reactor. The findings in this study will be helpful in developing the integrated treatment system to achieve low-cost excess sludge minimisation.

A neural networks-based drug discovery approach and its application for designing aldose reductase inhibitors

A novel approach that combines neural networks, computer docking and quantum mechanical method is developed to design potent aldose reductase inhibitors (ARIs). Neural networks is employed to determine the quantitative structure-activity relationship (QSAR) among the known ARIs. The physical descriptors of the neural networks, such as electronegativity and molar volume, are evaluated with first-principles quantum mechanical method. Based on the QSAR, new candidates for ARI are predicted, and subsequently screened via computer docking technique. The surviving candidates are further tested via quantum mechanical calculation for their bindings to aldose reductase. We find that the best 49 predicted ARI candidates have better calculated binding energies than those of experimentally known drug candidates.

Accurate prediction of heat of formation by combining Hartree–Fock/density functional theory calculation with linear regression correction approach

A linear regression correction approach has been developed successfully to account for the electron correlation energy missing in Hartree-Fock calculation and to reduce the calculation errors of density functional theory. The numbers of lone-pair electrons, bonding electrons and inner layer electrons in molecules, and the number of unpaired electrons in the composing atoms in their ground states are chosen to be the most important physical descriptors to determine the correlation energy unaccounted by Hartree-Fock method or to improve the results calculated by B3LYP density functional theory method. As a demonstration, this proposed linear regression correction approach has been applied to evaluate the standard heats of formation DeltaH(f) (Theta) of 180 small-sized to medium-sized organic molecules at 298.15 K. Upon correction, the mean absolute deviation for the 150 molecules in the training set decreases from 351.0 to 4.6 kcal/mol and 360.9 to 4.6 kcal/mol for HF/6-31G(d) and HF/6-311+G(d,p) methods, respectively. For B3LYP method, the mean absolute deviations are reduced from 9.2 and 18.2 kcal/mol to 2.7 and 2.4 kcal/mol for 6-31G(d) and 6-311+G(d,p) basis sets, respectively.

Quantum-mechanical investigation of field-emission mechanism of a micrometer-long single-walled carbon nanotube

A quantum-mechanical simulation is carried out to investigate the charge distribution and electrostatic potential along a 1 microm long (5,5) single-walled carbon nanotube under realistic field-emission experimental conditions. A single layer of carbon atoms is found sufficient to shield most of the electric field except at the tip where strong field penetration occurs. The penetration leads to a nonlinear decrease of potential barrier for emission, which is equally responsible for the low threshold voltage besides the well-known geometrical field enhancement factor.